X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=d6be4e4f1a16e00af29cfe36052c98e3a6e98efb;hp=7bcb4e41185bfa2104b3ef29432db0af7cbe58a2;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff diff --git a/engine.cpp b/engine.cpp index 7bcb4e4..d6be4e4 100644 --- a/engine.cpp +++ b/engine.cpp @@ -25,14 +25,19 @@ Engine::Engine(){ exit(1); } } +/***********************************************************************/ /***********************************************************************/ InteractEngine::InteractEngine(string path){ - globaldata = GlobalData::getInstance(); - globaldata->argv = path; + string temppath = path.substr(0, (path.find_last_of("othur")-5)); + + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + + mout->argv = path; } /***********************************************************************/ @@ -51,17 +56,52 @@ bool InteractEngine::getInput(){ while(quitCommandCalled != 1){ - + #ifdef USE_MPI + int pid, processors; + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + + #endif + + if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); } + mout->mothurOutEndLine(); input = getCommand(); mout->mothurOutEndLine(); - + if (mout->control_pressed) { input = "quit()"; } //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } + + #ifdef USE_MPI + //send commandName + for(int i = 1; i < processors; i++) { + int length = input.length(); + MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + + } + }else { + int length; + MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //recieve container + char* tempBuf = new char[length]; + MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + + input = tempBuf; + if (input.length() > length) { input = input.substr(0, length); } + delete tempBuf; + } + + + #endif + CommandOptionParser parser(input); commandName = parser.getCommandString(); @@ -72,13 +112,31 @@ bool InteractEngine::getInput(){ #ifdef USE_MPI int pid; MPI_Comm_rank(MPI_COMM_WORLD, &pid); - -//cout << pid << " is here " << commandName << endl; + if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { + //cout << pid << " is in execute " << commandName << endl; #endif //executes valid command + mout->changedSeqNames = false; + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->commandInputsConvertError = false; + mout->printedSharedHeaders = false; + mout->currentSharedBinLabels.clear(); + mout->sharedBinLabelsInFile.clear(); + mout->printedListHeaders = false; + mout->listBinLabelsInFile.clear(); + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } + + //if we aborted command + if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } + mout->control_pressed = 0; mout->executing = false; @@ -100,18 +158,15 @@ bool InteractEngine::getInput(){ /***********************************************************************/ string Engine::getCommand() { try { - #ifdef USE_MPI - MPI_Barrier(MPI_COMM_WORLD); - #endif - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) #ifdef USE_READLINE char* nextCommand = NULL; nextCommand = readline("mothur > "); if(nextCommand != NULL) { add_history(nextCommand); } else{ //^D causes null string and we want it to quit mothur - nextCommand = "quit"; + nextCommand = strdup("quit"); mout->mothurOut(nextCommand); } @@ -146,10 +201,15 @@ string Engine::getCommand() { //This function opens the batchfile to be used by BatchEngine::getInput. BatchEngine::BatchEngine(string path, string batchFileName){ try { - globaldata = GlobalData::getInstance(); - openedBatch = openInputFile(batchFileName, inputBatchFile); - globaldata->argv = path; + openedBatch = mout->openInputFile(batchFileName, inputBatchFile); + + string temppath = path.substr(0, (path.find_last_of("othur")-5)); + + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + + mout->argv = path; } catch(exception& e) { @@ -180,13 +240,48 @@ bool BatchEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; int count = 0; - while(quitCommandCalled == 0){ - + while(quitCommandCalled != 1){ + + #ifdef USE_MPI + int pid, processors; + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + + #endif + input = getNextCommand(inputBatchFile); count++; + #ifdef USE_MPI + //send commandName + for(int i = 1; i < processors; i++) { + int length = input.length(); + MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + + } + }else { + int length; + MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //recieve container + char* tempBuf = new char[length]; + MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + + input = tempBuf; + if (input.length() > length) { input = input.substr(0, length); } + delete tempBuf; + } + + + #endif + + + if (input[0] != '#') { - + if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); } mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); @@ -210,8 +305,27 @@ bool BatchEngine::getInput(){ if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { #endif //executes valid command + mout->changedSeqNames = false; + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->commandInputsConvertError = false; + mout->printedSharedHeaders = false; + mout->currentSharedBinLabels.clear(); + mout->sharedBinLabelsInFile.clear(); + mout->printedListHeaders = false; + mout->listBinLabelsInFile.clear(); + + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } + + //if we aborted command + if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } + mout->control_pressed = 0; mout->executing = false; @@ -224,7 +338,7 @@ bool BatchEngine::getInput(){ } } - gobble(inputBatchFile); + mout->gobble(inputBatchFile); } inputBatchFile.close(); @@ -238,16 +352,11 @@ bool BatchEngine::getInput(){ /***********************************************************************/ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { try { - - #ifdef USE_MPI - int err = MPI_Barrier(MPI_COMM_WORLD); -//cout << "barrier = " << err << '\t' << MPI_SUCCESS << endl; - #endif - + string nextcommand = ""; if (inputBatchFile.eof()) { nextcommand = "quit()"; } - else { nextcommand = getline(inputBatchFile); } + else { nextcommand = mout->getline(inputBatchFile); } return nextcommand; } @@ -262,12 +371,16 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) { //This function opens the batchfile to be used by BatchEngine::getInput. ScriptEngine::ScriptEngine(string path, string commandString){ try { - globaldata = GlobalData::getInstance(); //remove quotes listOfCommands = commandString.substr(1, (commandString.length()-1)); + + string temppath = path.substr(0, (path.find_last_of("othur")-5)); - globaldata->argv = path; + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + + mout->argv = path; } catch(exception& e) { @@ -293,15 +406,55 @@ bool ScriptEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - while(quitCommandCalled == 0){ - + while(quitCommandCalled != 1){ + + #ifdef USE_MPI + int pid, processors; + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + + #endif + input = getNextCommand(listOfCommands); if (input == "") { input = "quit()"; } + + if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); } + + if (mout->gui) { + if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {} + else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {} + else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); } + }else{ + mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); + } + + #ifdef USE_MPI + //send commandName + for(int i = 1; i < processors; i++) { + int length = input.length(); + MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + + } + }else { + int length; + MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //recieve container + char* tempBuf = new char[length]; + MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + + input = tempBuf; + if (input.length() > length) { input = input.substr(0, length); } + delete tempBuf; + } + + + #endif - mout->mothurOutEndLine(); - mout->mothurOut("mothur > " + input); - mout->mothurOutEndLine(); if (mout->control_pressed) { input = "quit()"; } @@ -316,7 +469,6 @@ bool ScriptEngine::getInput(){ mout->executing = true; #ifdef USE_MPI int pid, numProcesses; - MPI_Status status; MPI_Comm_rank(MPI_COMM_WORLD, &pid); MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); @@ -326,8 +478,26 @@ bool ScriptEngine::getInput(){ //cout << pid << " is in execute" << endl; #endif //executes valid command + mout->changedSeqNames = false; + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->commandInputsConvertError = false; + mout->printedSharedHeaders = false; + mout->currentSharedBinLabels.clear(); + mout->sharedBinLabelsInFile.clear(); + mout->printedListHeaders = false; + mout->listBinLabelsInFile.clear(); + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } + + //if we aborted command + if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } + mout->control_pressed = 0; mout->executing = false; @@ -354,17 +524,18 @@ bool ScriptEngine::getInput(){ string ScriptEngine::getNextCommand(string& commandString) { try { - #ifdef USE_MPI - MPI_Barrier(MPI_COMM_WORLD); - #endif - string nextcommand = ""; int count = 0; + bool ignoreSemiColons = false; //go through string until you reach ; or end while (count < commandString.length()) { - if (commandString[count] == ';') { break; } + //you want to ignore any ; until you reach the next ' + if ((commandString[count] == '\'') && (!ignoreSemiColons)) { ignoreSemiColons = true; } + else if ((commandString[count] == '\'') && (ignoreSemiColons)) { ignoreSemiColons = false; } + + if ((commandString[count] == ';') && (!ignoreSemiColons)) { break; } else { nextcommand += commandString[count]; } count++;